search

Shamir-Lab / Recycler

This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, and Ron Shamir
BSD 3-Clause "New" or "Revised" License
58 stars 7 forks source link

RuntimeWarning: invalid value encountered in sqrt #28

Open Freemacl opened 6 years ago

Freemacl commented 6 years ago

This warning occurs for some of my files but not all.

~/anaconda3/lib/python3.6/site-packages/recycler-0.62-py3.6.egg/recyclelib/utils.py:178: RuntimeWarning: invalid value encountered in sqrt

after I issue the recycle.py command, It will run through several "# nodes remain in component" and eventually get stuck somewhere. I've tried letting it run for several hours, but it never progresses.

dpellow commented 6 years ago

Thanks for letting us know! What versions of Recycler and SPAdes are you working with? If you can send us an example where this happens we'll be able to look into it in more detail.

Rachael-16 commented 4 years ago

I have the same issue, it run through my first node then produces this error.

/home/rachael/anaconda2/lib/python2.7/site-packages/recyclelib/utils.py:178: RuntimeWarning: invalid value encountered in sqrt std = np.sqrt(np.dot(wgts,(covs-mean)**2)) (1092, ' nodes remain in component\n')

assembly graph was generated using Spades v3.13.1

Has a solution to this issue been identified?

dpellow commented 4 years ago

What version of Recycler are you using, have you pulled the most recent version? Also, note that our newer tool, SCAPP, may produce better results than Recycler

Rachael-16 commented 4 years ago

Hi I'm using Recycler v0.7, it was installed using conda.

I will try SCAPP, however I think it would nice to know what going wrong here.

dpellow commented 4 years ago

The error means that that line is trying to evaluate the square root of a negative number. The value should not be negative, I can't tell why it occurs without being able to reproduce the error. Can you check if the error is reproduced when installing the latest version of the tool from source (ie not using conda)?